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Acta Crystallogr Sect E Struct Rep Online. 2009 October 1; 65(Pt 10): m1223.
Published online 2009 September 19. doi:  10.1107/S1600536809036939
PMCID: PMC2970219

Poly[[bis­[μ2-8-ethyl-5-oxo-2-(piperazin-1-yl)-5,8-dihydro­pyrido[2,3-d]pyrimidine-6-carboxyl­ato]zinc(II)] dihydrate]

Abstract

The title compound, {[Zn(C14H16N5O3)2]·2H2O}n or [Zn(ppa)2]·2H2O}n, where ppa = 8-ethyl-5,8-dihydro-5-oxo-2-(1-piperazin­yl)-pyrido(2,3-d)-pyrimidine-6-carboxyl­ate, was synthesized under hydro­thermal conditions. The ZnII atom (site symmetry An external file that holds a picture, illustration, etc.
Object name is e-65-m1223-efi1.jpg) exhibits a distorted trans-ZnN2O4 octa­hedral geometry defined by two monodentate N-bonded and two bidentate O,O-bonded ppa monoanions. The extended two-dimensional structure arising from this connectivity is a square grid and the disordered uncoordinated water mol­ecules occupy cavities within the grid. An N—H(...)O hydrogen bond occurs.

Related literature

For manganese complexes of the ppa anion, see: Huang et al. (2008 [triangle]). For background to the medicinal uses of pipemidic acid, see: Mizuki et al. (1996 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-m1223-scheme1.jpg

Experimental

Crystal data

  • [Zn(C14H16N5O3)2]·2H2O
  • M r = 704.05
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-m1223-efi2.jpg
  • a = 6.1146 (12) Å
  • b = 21.424 (4) Å
  • c = 12.577 (3) Å
  • β = 101.10 (3)°
  • V = 1616.9 (6) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.82 mm−1
  • T = 295 K
  • 0.36 × 0.28 × 0.18 mm

Data collection

  • Rigaku R-AXIS RAPID diffractometer
  • Absorption correction: multi-scan (CrystalStructure; Rigaku/MSC, 2002 [triangle]) T min = 0.756, T max = 0.866
  • 15697 measured reflections
  • 3684 independent reflections
  • 2570 reflections with I > 2σ(I)
  • R int = 0.045

Refinement

  • R[F 2 > 2σ(F 2)] = 0.057
  • wR(F 2) = 0.210
  • S = 1.06
  • 3684 reflections
  • 228 parameters
  • 1 restraint
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.83 e Å−3
  • Δρmin = −0.83 e Å−3

Data collection: RAPID-AUTO (Rigaku, 1998 [triangle]); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002 [triangle]); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEPII (Johnson, 1976 [triangle]); software used to prepare material for publication: SHELXL97.

Table 1
Selected bond lengths (Å)
Table 2
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809036939/hb5062sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809036939/hb5062Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The authors thank the Innovation Science Foundation of Harbin Medical University for financial support (grant No. 060041).

supplementary crystallographic information

Comment

Pipemidic acid (Hppa, C14H16N5O3, 8-Ethyl-5,8-dihydro-5-oxo-2- (1-piperazinyl)-pyrido(2,3 - d)-pyrimidine-6-carboxylic acid) is member of a class of quinolones used to treat infections (Mizuki et al., 1996). The manganese complex of the ppa anion has been reported (Huang et al., 2008); the title zinc(II) complex is reported here (Fig. 1).

The zinc(II) atom is coordinated by four oxygen atoms and two N atoms from four ppa ligands (two monodentate-N and two O,O-bidentate) to form a square grid (Fig. 2). The disordered, uncoordinated, water molecules occupy the cavities.

Experimental

A mixture of Zn(CH3COO)2.2H2O (0.055 g, 0.25 mmol), Hppa (0.15 g, 0.5 mmol), sodium hydroxide (0.04 g, 1 mmol) and water (12 ml) was stirred for 30 min in air. The mixture was then transferred to a 23 ml Teflon-lined hydrothermal bomb. The bomb was kept at 433 K for 72 h under autogenous pressure. Upon cooling, colourless prisms of (I) were obtained from the reaction mixture.

Refinement

The carbon-bound H atoms were positioned geometrically (C—H = 0.93–0.97 Å) and were included in the refinement in the riding model approximation, with Uiso(H) = 1.2Ueq(C). The H on Nitrogen atoms were located in a difference Fourier map, and were refined with a distance restraint of N—H = 0.86 (1)Å and with Uiso(H) = 1.2Ueq(N).

The water H atoms could not be placed due to the disorder of the O atoms.

Figures

Fig. 1.
The asymmetric unit of (I) extended to show the zinc coordination sphere showing the showing 50% displacement ellipsoids (water molecule O atoms have been omitted for clarity).
Fig. 2.
A view of part of a two-dimensional polymeric sheet in (I) showing the square-grid connectivity (H atoms and water molecule O atoms omitted for clarity).

Crystal data

[Zn(C14H16N5O3)2]·2H2OZ = 2
Mr = 704.05F(000) = 728
Monoclinic, P21/cDx = 1.442 Mg m3
Hall symbol: -P 2ybcMo Kα radiation, λ = 0.71073 Å
a = 6.1146 (12) ŵ = 0.82 mm1
b = 21.424 (4) ÅT = 295 K
c = 12.577 (3) ÅPrism, colorless
β = 101.10 (3)°0.36 × 0.28 × 0.18 mm
V = 1616.9 (6) Å3

Data collection

Rigaku R-AXIS RAPID diffractometer3684 independent reflections
Radiation source: fine-focus sealed tube2570 reflections with I > 2σ(I)
graphiteRint = 0.045
Detector resolution: 10.000 pixels mm-1θmax = 27.5°, θmin = 3.3°
ω scansh = −7→7
Absorption correction: multi-scan (CrystalStructure; Rigaku/MSC, 2002)k = −27→25
Tmin = 0.756, Tmax = 0.866l = −16→16
15697 measured reflections

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.057Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.210H atoms treated by a mixture of independent and constrained refinement
S = 1.06w = 1/[σ2(Fo2) + (0.1254P)2 + 1.7801P] where P = (Fo2 + 2Fc2)/3
3684 reflections(Δ/σ)max < 0.001
228 parametersΔρmax = 0.83 e Å3
1 restraintΔρmin = −0.83 e Å3

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.
Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

xyzUiso*/UeqOcc. (<1)
O1W−0.045 (3)−0.0632 (10)−0.0746 (11)0.187 (8)0.50
O2W0.340 (5)0.0205 (10)−0.0364 (12)0.251 (14)0.50
Zn10.50000.00000.50000.0265 (2)
O10.6981 (4)−0.00325 (10)0.3877 (2)0.0271 (6)
O20.8573 (7)0.01818 (18)0.2500 (3)0.0616 (11)
O30.3495 (5)0.07935 (11)0.4179 (2)0.0317 (6)
N10.4916 (7)0.17173 (17)0.1532 (3)0.0481 (10)
N20.2252 (6)0.24690 (15)0.1677 (3)0.0386 (8)
N3−0.0127 (6)0.23572 (16)0.2988 (3)0.0436 (9)
N4−0.0227 (6)0.32384 (15)0.1907 (3)0.0349 (8)
N5−0.2450 (5)0.43908 (14)0.1084 (2)0.0273 (7)
H5N−0.154 (8)0.466 (2)0.152 (4)0.065 (16)*
C10.7147 (7)0.02891 (17)0.3064 (3)0.0316 (8)
C20.5658 (7)0.08450 (17)0.2772 (3)0.0317 (8)
C30.3947 (6)0.10453 (16)0.3346 (3)0.0271 (7)
C40.2744 (7)0.15974 (16)0.2910 (3)0.0303 (8)
C50.0937 (8)0.18359 (19)0.3318 (3)0.0398 (10)
H50.04540.16100.38610.048*
C60.0671 (7)0.26762 (18)0.2197 (3)0.0327 (8)
C70.3246 (7)0.19340 (18)0.2034 (3)0.0360 (9)
C80.6010 (8)0.1189 (2)0.1902 (4)0.0457 (11)
H80.70960.10470.15350.055*
C90.5540 (11)0.2051 (3)0.0585 (5)0.0665 (16)
H9B0.53060.24960.06530.080*
H9A0.71070.19830.05820.080*
C100.4247 (16)0.1834 (5)−0.0401 (7)0.116 (3)
H10C0.45660.1401−0.04960.174*
H10B0.46050.2071−0.09930.174*
H10A0.26930.1883−0.03850.174*
C11−0.1608 (8)0.3572 (2)0.2553 (4)0.0475 (11)
H11B−0.06730.38390.30770.057*
H11A−0.23460.32750.29470.057*
C12−0.3356 (7)0.3970 (2)0.1813 (4)0.0398 (10)
H12B−0.44290.36940.13790.048*
H12A−0.41500.42180.22620.048*
C13−0.1090 (6)0.40176 (17)0.0469 (3)0.0317 (8)
H13A−0.04050.42950.00180.038*
H13B−0.20570.3734−0.00060.038*
C140.0708 (7)0.36460 (18)0.1185 (4)0.0369 (9)
H14B0.15000.33970.07370.044*
H14A0.17680.39290.16100.044*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O1W0.209 (18)0.28 (2)0.094 (9)−0.004 (16)0.091 (11)0.013 (12)
O2W0.47 (4)0.202 (17)0.077 (9)0.11 (2)0.049 (16)−0.057 (12)
Zn10.0317 (4)0.0194 (3)0.0294 (3)0.0006 (2)0.0079 (2)0.0028 (2)
O10.0276 (13)0.0218 (12)0.0333 (14)0.0019 (9)0.0089 (10)0.0029 (10)
O20.073 (3)0.062 (2)0.060 (2)0.040 (2)0.0387 (19)0.0275 (18)
O30.0378 (15)0.0223 (12)0.0368 (14)0.0092 (10)0.0116 (11)0.0121 (11)
N10.065 (3)0.0398 (19)0.046 (2)0.0223 (18)0.0265 (19)0.0195 (17)
N20.051 (2)0.0282 (16)0.0400 (18)0.0135 (15)0.0160 (16)0.0124 (14)
N30.044 (2)0.0361 (18)0.055 (2)0.0166 (16)0.0219 (17)0.0231 (17)
N40.0390 (19)0.0283 (16)0.0415 (18)0.0096 (14)0.0177 (15)0.0119 (14)
N50.0265 (16)0.0219 (14)0.0324 (15)0.0064 (12)0.0028 (12)0.0034 (13)
C10.037 (2)0.0274 (18)0.0316 (18)0.0046 (15)0.0112 (16)−0.0002 (16)
C20.038 (2)0.0238 (17)0.0354 (19)0.0070 (15)0.0110 (16)0.0035 (15)
C30.0283 (18)0.0219 (16)0.0302 (17)0.0007 (13)0.0032 (14)0.0013 (14)
C40.036 (2)0.0242 (17)0.0318 (18)0.0021 (15)0.0087 (15)0.0055 (15)
C50.048 (3)0.033 (2)0.043 (2)0.0088 (18)0.0188 (19)0.0174 (18)
C60.033 (2)0.0273 (18)0.0380 (19)0.0046 (15)0.0078 (16)0.0077 (16)
C70.044 (2)0.0323 (19)0.0347 (19)0.0092 (17)0.0137 (17)0.0067 (17)
C80.060 (3)0.037 (2)0.046 (2)0.018 (2)0.026 (2)0.0107 (19)
C90.083 (4)0.063 (3)0.062 (3)0.030 (3)0.038 (3)0.024 (3)
C100.117 (7)0.144 (9)0.090 (5)0.031 (6)0.028 (5)0.024 (6)
C110.055 (3)0.045 (2)0.047 (2)0.025 (2)0.021 (2)0.020 (2)
C120.040 (2)0.036 (2)0.047 (2)0.0157 (17)0.0179 (18)0.0161 (19)
C130.035 (2)0.0247 (17)0.0366 (19)0.0101 (15)0.0094 (16)0.0081 (15)
C140.033 (2)0.0293 (18)0.051 (2)0.0043 (16)0.0147 (17)0.0119 (18)

Geometric parameters (Å, °)

Zn1—O12.031 (3)C2—C81.370 (6)
Zn1—O1i2.031 (3)C2—C31.446 (5)
Zn1—O3i2.107 (2)C3—C41.444 (5)
Zn1—O32.107 (2)C4—C71.399 (5)
Zn1—N5ii2.275 (3)C4—C51.401 (6)
Zn1—N5iii2.275 (3)C5—H50.9300
O1—C11.253 (5)C8—H80.9300
O2—C11.247 (5)C9—C101.415 (11)
O3—C31.256 (4)C9—H9B0.9700
N1—C81.351 (5)C9—H9A0.9700
N1—C71.381 (5)C10—H10C0.9600
N1—C91.500 (6)C10—H10B0.9600
N2—C71.334 (5)C10—H10A0.9600
N2—C61.343 (5)C11—C121.534 (5)
N3—C51.319 (5)C11—H11B0.9700
N3—C61.373 (5)C11—H11A0.9700
N4—C61.345 (5)C12—H12B0.9700
N4—C141.454 (5)C12—H12A0.9700
N4—C111.466 (5)C13—C141.508 (5)
N5—C121.468 (5)C13—H13A0.9700
N5—C131.475 (5)C13—H13B0.9700
N5—Zn1iv2.275 (3)C14—H14B0.9700
N5—H5N0.900 (10)C14—H14A0.9700
C1—C21.501 (5)
O1—Zn1—O1i180.0N2—C6—N4117.3 (3)
O1—Zn1—O3i92.90 (10)N2—C6—N3125.3 (4)
O1i—Zn1—O3i87.10 (10)N4—C6—N3117.3 (4)
O1—Zn1—O387.10 (10)N2—C7—N1117.6 (3)
O1i—Zn1—O392.90 (10)N2—C7—C4123.6 (4)
O3i—Zn1—O3180.0N1—C7—C4118.7 (3)
O1—Zn1—N5ii89.74 (11)N1—C8—C2125.6 (4)
O1i—Zn1—N5ii90.26 (11)N1—C8—H8117.2
O3i—Zn1—N5ii90.86 (11)C2—C8—H8117.2
O3—Zn1—N5ii89.14 (11)C10—C9—N1110.8 (7)
O1—Zn1—N5iii90.26 (11)C10—C9—H9B109.5
O1i—Zn1—N5iii89.74 (11)N1—C9—H9B109.5
O3i—Zn1—N5iii89.14 (11)C10—C9—H9A109.5
O3—Zn1—N5iii90.86 (11)N1—C9—H9A109.5
N5ii—Zn1—N5iii180.0H9B—C9—H9A108.1
C1—O1—Zn1134.5 (2)C9—C10—H10C109.5
C3—O3—Zn1127.6 (2)C9—C10—H10B109.5
C8—N1—C7119.0 (3)H10C—C10—H10B109.5
C8—N1—C9119.2 (4)C9—C10—H10A109.5
C7—N1—C9121.8 (4)H10C—C10—H10A109.5
C7—N2—C6116.3 (3)H10B—C10—H10A109.5
C5—N3—C6115.3 (4)N4—C11—C12110.0 (3)
C6—N4—C14121.2 (3)N4—C11—H11B109.7
C6—N4—C11122.4 (3)C12—C11—H11B109.7
C14—N4—C11113.0 (3)N4—C11—H11A109.7
C12—N5—C13108.3 (3)C12—C11—H11A109.7
C12—N5—Zn1iv115.4 (2)H11B—C11—H11A108.2
C13—N5—Zn1iv112.8 (2)N5—C12—C11114.7 (3)
C12—N5—H5N106 (4)N5—C12—H12B108.6
C13—N5—H5N108 (4)C11—C12—H12B108.6
Zn1iv—N5—H5N106 (4)N5—C12—H12A108.6
O2—C1—O1122.6 (4)C11—C12—H12A108.6
O2—C1—C2117.7 (3)H12B—C12—H12A107.6
O1—C1—C2119.7 (3)N5—C13—C14113.1 (3)
C8—C2—C3118.6 (3)N5—C13—H13A109.0
C8—C2—C1116.2 (3)C14—C13—H13A109.0
C3—C2—C1125.2 (3)N5—C13—H13B109.0
O3—C3—C4119.4 (3)C14—C13—H13B109.0
O3—C3—C2125.8 (3)H13A—C13—H13B107.8
C4—C3—C2114.7 (3)N4—C14—C13111.2 (3)
C7—C4—C5114.1 (3)N4—C14—H14B109.4
C7—C4—C3123.2 (4)C13—C14—H14B109.4
C5—C4—C3122.6 (3)N4—C14—H14A109.4
N3—C5—C4124.7 (4)C13—C14—H14A109.4
N3—C5—H5117.6H14B—C14—H14A108.0
C4—C5—H5117.6
O1i—Zn1—O1—C1−50 (2)C11—N4—C6—N2−167.0 (4)
O3i—Zn1—O1—C1179.5 (4)C14—N4—C6—N3171.7 (4)
O3—Zn1—O1—C1−0.5 (4)C11—N4—C6—N314.0 (6)
N5ii—Zn1—O1—C188.7 (4)C5—N3—C6—N27.0 (7)
N5iii—Zn1—O1—C1−91.3 (4)C5—N3—C6—N4−174.0 (4)
O1—Zn1—O3—C30.4 (3)C6—N2—C7—N1−178.5 (4)
O1i—Zn1—O3—C3−179.6 (3)C6—N2—C7—C4−1.0 (6)
O3i—Zn1—O3—C365 (100)C8—N1—C7—N2177.5 (4)
N5ii—Zn1—O3—C3−89.4 (3)C9—N1—C7—N2−2.7 (7)
N5iii—Zn1—O3—C390.6 (3)C8—N1—C7—C4−0.1 (7)
Zn1—O1—C1—O2178.2 (3)C9—N1—C7—C4179.7 (5)
Zn1—O1—C1—C21.0 (6)C5—C4—C7—N26.2 (6)
O2—C1—C2—C8−0.1 (6)C3—C4—C7—N2−174.9 (4)
O1—C1—C2—C8177.1 (4)C5—C4—C7—N1−176.3 (4)
O2—C1—C2—C3−178.8 (4)C3—C4—C7—N12.5 (6)
O1—C1—C2—C3−1.6 (6)C7—N1—C8—C2−1.9 (8)
Zn1—O3—C3—C4−179.0 (2)C9—N1—C8—C2178.3 (5)
Zn1—O3—C3—C2−1.1 (5)C3—C2—C8—N11.4 (7)
C8—C2—C3—O3−177.0 (4)C1—C2—C8—N1−177.4 (4)
C1—C2—C3—O31.7 (6)C8—N1—C9—C1090.7 (7)
C8—C2—C3—C41.0 (6)C7—N1—C9—C10−89.1 (7)
C1—C2—C3—C4179.7 (4)C6—N4—C11—C12−148.9 (4)
O3—C3—C4—C7175.2 (4)C14—N4—C11—C1251.8 (5)
C2—C3—C4—C7−2.9 (6)C13—N5—C12—C1153.7 (5)
O3—C3—C4—C5−6.0 (6)Zn1iv—N5—C12—C11−178.8 (3)
C2—C3—C4—C5175.9 (4)N4—C11—C12—N5−52.7 (5)
C6—N3—C5—C4−0.8 (7)C12—N5—C13—C14−55.0 (4)
C7—C4—C5—N3−5.2 (7)Zn1iv—N5—C13—C14176.0 (2)
C3—C4—C5—N3175.9 (4)C6—N4—C14—C13145.9 (4)
C7—N2—C6—N4174.8 (4)C11—N4—C14—C13−54.5 (5)
C7—N2—C6—N3−6.2 (7)N5—C13—C14—N456.5 (5)
C14—N4—C6—N2−9.3 (6)

Symmetry codes: (i) −x+1, −y, −z+1; (ii) −x, y−1/2, −z+1/2; (iii) x+1, −y+1/2, z+1/2; (iv) −x, y+1/2, −z+1/2.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N5—H5N···O2v0.91 (5)2.28 (5)3.168 (5)166 (4)

Symmetry codes: (v) −x+1, y+1/2, −z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HB5062).

References

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